This GST compliance handbook for Indian startups covers everything a funded founder needs to know about GST registration, GST filing, TDS, and ROC compliance in 2026 — including exactly which filings are mandatory, when they are due, and what Komplai Managed handles automatically so founders do not have to track them manually. Whether you are registering for GST for the first time or trying to understand why you missed a deadline, this guide gives you the complete picture.
GST Registration: When It Is Mandatory and When It Is Beneficial
GST registration is mandatory for Indian startups that cross the registration threshold: ₹40 lakh aggregate annual turnover for businesses supplying goods, and ₹20 lakh for businesses supplying services. For startups in special category states (including Manipur, Meghalaya, Mizoram, Nagaland, Arunachal Pradesh, Tripura, and Sikkim), the threshold is ₹10 lakh for services.
However, mandatory thresholds are not the only reason startups register. Voluntary GST registration is strongly recommended — and in practice, usually necessary — for any startup that sells to GST-registered businesses. B2B customers cannot claim input tax credit (ITC) on purchases from an unregistered supplier, which makes an unregistered startup effectively more expensive as a vendor than a registered competitor charging the same pre-tax price. According to ClearTax, 84% of Indian B2B startups register for GST voluntarily before crossing the mandatory threshold — the commercial pressure from B2B customers makes voluntary registration economically necessary.
The GST registration process involves: filing Form GST REG-01 on the GSTN portal, providing proof of business registration (Certificate of Incorporation for Pvt Ltd), PAN card, proof of business address, bank account details, and the authorised signatory’s Aadhaar. The GSTN portal typically processes applications within 7–10 working days. A GSTIN (Goods and Services Tax Identification Number) is issued upon approval — a unique 15-digit number that identifies the registered business for all GST purposes. For the comprehensive list of every compliance obligation a private limited company must handle, see our guide to what compliance a private limited company in India actually needs to handle.
Can a Startup Do Business Without GST Registration?
A startup can technically operate without GST registration if it is below the mandatory threshold and sells only to consumers (B2C). However, operating without registration has three practical consequences that most founders underestimate.
First, as noted above, B2B customers cannot claim ITC on purchases from unregistered suppliers. For any startup selling to businesses — which includes the vast majority of funded B2B SaaS, services, and marketplace companies — this makes the startup a commercially inferior choice compared to registered competitors, regardless of product quality or pricing.
Second, unregistered startups cannot claim ITC on their own purchases. Every vendor payment — cloud hosting, office rent, software subscriptions — includes embedded GST that a registered business can reclaim. An unregistered business absorbs these costs as final expenses. At scale, the ITC benefit of registration substantially offsets the compliance overhead of filing.
Third, if a startup grows past the threshold without registering, it must register retroactively — and may face penalties for the period of operation above the threshold without registration. Given that most funded startups plan to grow past the threshold, voluntary early registration is almost always the right choice. For a worked example of compliance costs across stages, see our complete guide to managed finance for Indian startups in 2026.
GST Filing: The Complete Monthly and Quarterly Calendar
Once registered, a GST-registered startup must file returns on a monthly or quarterly schedule, depending on the filing scheme. Most funded startups file monthly under the regular scheme. The key filing deadlines are as follows.
GSTR-1 (outward supplies): Filed by the 11th of every month (monthly filers) or by the 13th of the month following each quarter (quarterly filers). GSTR-1 declares all invoices issued to GST-registered customers — the tax the startup has collected on behalf of the government. Errors in GSTR-1 affect the ITC of customers and create reconciliation problems.
GSTR-3B (summary return + tax payment): Filed by the 20th of every month for most taxpayers (the deadline varies slightly by state). GSTR-3B summarises total outward supplies, total inward supplies eligible for ITC, and the net tax payable. Tax must be paid at the time of filing — late payment attracts interest at 18% per annum plus a ₹50/day late fee.
GSTR-9 (annual return): Filed by December 31st of the following financial year (so GSTR-9 for FY 2024–25 is due by December 31, 2025). GSTR-9 reconciles the entire year’s GST transactions and must match the monthly GSTR-1 and GSTR-3B filings. Discrepancies between GSTR-9 and the monthly returns trigger GST notices.
GSTR-9C (reconciliation statement): Required for taxpayers with annual aggregate turnover above ₹5Cr. This is a certified reconciliation statement between the annual return and the audited financial statements — prepared by a CA or cost accountant. For a detailed walkthrough of every filing deadline across the compliance calendar, see our startup compliance calendar for India in 2026.
TDS Compliance: What Startups Must Deduct and When
Tax Deducted at Source (TDS) is a separate compliance obligation from GST. Under the Income Tax Act, any company making certain payments above specified thresholds must deduct TDS at the applicable rate and deposit it to the government.
The most common TDS obligations for Indian startups are: TDS on contractor payments (Section 194C — 1% for individual/HUF contractors, 2% for others, threshold ₹30,000 per transaction or ₹1L cumulative in a year); TDS on professional fees (Section 194J — 10% on fees paid to lawyers, consultants, and other professionals, threshold ₹30,000); TDS on rent above ₹2.4L per year (Section 194I — 10% for land/building, 2% for plant/machinery); and TDS on salary (Section 192 — deducted at applicable income tax slab rates for each employee).
The TDS deposit deadline is the 7th of the month following the month in which the deduction was made — except for March deductions, which must be deposited by April 30th. Quarterly TDS returns (Form 26Q for non-salary payments, Form 24Q for salary) are due by July 31, October 31, January 31, and May 31. Failure to deduct TDS or failure to deposit deducted TDS attracts interest at 1–1.5% per month and may be treated as a default under Section 201. According to the Income Tax Department, TDS defaults are the most common compliance issue for private limited companies in India — and the penalties compound quickly across multiple vendor payments.
ROC Compliance: The Corporate Filings Every Startup Must Make
Beyond GST and TDS, every private limited company incorporated in India must maintain ongoing compliance with the Ministry of Corporate Affairs (MCA) through the Registrar of Companies (ROC). These filings are mandatory regardless of the company’s revenue or GST status.
The core annual ROC filings are: AOC-4 (annual accounts filing — due by November 29th, within 30 days of the AGM, or within 60 days of the financial year end if no AGM has been held); MGT-7 or MGT-7A (annual return filing — due by November 28th for most companies, within 60 days of the AGM); and DIR-3 KYC (director KYC — every director must file DIR-3 KYC annually by September 30th).
Additionally, companies with paid-up share capital above ₹5Cr or turnover above ₹20Cr must appoint a Company Secretary. Companies with paid-up capital above ₹10Cr or turnover above ₹100Cr require a statutory audit by a Chartered Accountant. For startups that have raised funding, the paid-up capital and turnover thresholds often trigger these requirements earlier than founders expect. Missing ROC deadlines attracts penalties of ₹100/day per filing, which compound quickly across multiple missed deadlines. For a startup that has missed multiple filings, the rectification cost can be significant — and any pending ROC defaults will surface immediately in investor due diligence. For more on what due diligence actually examines, see our diligence readiness checklist from incorporation to Series B.
How Komplai Managed Handles All Compliance Automatically
Komplai Managed’s Complete and Full Service tiers handle every compliance filing described in this guide — without founder involvement in the filing process. The AI automation layer tracks 75+ statutory deadlines across GST, TDS, and ROC obligations. The Forward-Deployed Accountant (FDA) reviews every filing before submission, applying the Maker-Checker model to ensure accuracy before the return is filed.
Specifically, Komplai Managed Complete covers: GSTR-1 and GSTR-3B monthly filing, GST ITC reconciliation with GSTR-2B, TDS deduction tracking and monthly deposit, quarterly TDS return filing (Form 26Q and 24Q), and annual GSTR-9 preparation. Komplai Managed Full Service additionally covers: ROC annual filings (AOC-4, MGT-7), DIR-3 KYC for all directors, secretarial compliance, and statutory audit coordination.
The critical advantage of Komplai Managed over a CA retainer for compliance is the early-warning system. Komplai Managed flags upcoming deadlines 7 days in advance and provides the current status of each filing — whether data is complete, whether there are open items, and whether the filing is on track for on-time submission. Most CA retainers file on or near the deadline, leaving no buffer for data issues or errors. Komplai Managed builds the buffer in by design. For the complete breakdown of what each tier covers and at what cost, see our complete guide to managed finance for Indian startups in 2026.
GST Input Tax Credit: The Most Common Mistake Indian Startups Make
Input tax credit (ITC) is the GST paid on purchases that a registered business can offset against the GST collected on sales. For a startup paying 18% GST on cloud infrastructure, software subscriptions, office rent, and professional services, ITC reclaim can represent ₹2–5L per month at Series A scale — a material cash flow benefit that many startups fail to claim correctly.
The most common ITC mistakes are: claiming ITC for invoices where the vendor has not filed their GSTR-1 (ITC is only available if the purchase appears in the startup’s GSTR-2B — auto-populated from the vendor’s filing); claiming ITC on blocked categories (cars, club memberships, personal expenses are not eligible); and failing to reconcile GSTR-2B against the books monthly, which leads to either under-claiming (cash left on the table) or over-claiming (which triggers notices and penalties).
Komplai Managed reconciles GSTR-2B against the startup’s purchase ledger monthly, ensuring ITC is claimed correctly on all eligible purchases and no ITC is claimed on blocked or unconfirmed purchases. The reconciliation is a standard part of the month-end close — not an add-on service. For a complete explanation of what each month-end close covers in Komplai Managed, see our guide to how Indian startups keep clean books without a finance team.
The Bottom Line
GST and compliance for Indian startups in 2026 involves three overlapping obligation streams — GST filing (monthly GSTR-1 and GSTR-3B, annual GSTR-9), TDS compliance (monthly deposits, quarterly returns), and ROC filings (annual accounts, annual return, director KYC) — each with its own deadlines, penalties, and data requirements. Managing these manually is a significant time cost; missing deadlines is a compounding financial cost.
Komplai Managed handles all three streams automatically — 75+ deadlines tracked, every filing reviewed by a Forward-Deployed Accountant before submission, zero missed deadlines. The Complete tier starts at an accessible monthly fee and covers the full GST + TDS compliance stack. Explore Komplai Managed to see which tier matches your startup’s current compliance requirements. And if you want an instant answer to “Which GST filings are we behind on?” — ask Larry.
Frequently Asked Questions
When must an Indian startup register for GST?
GST registration is mandatory when a startup’s aggregate annual turnover crosses ₹40 lakh (goods) or ₹20 lakh (services). In special category states, the threshold is ₹10 lakh for services. However, most B2B startups register voluntarily before crossing the threshold — B2B customers cannot claim ITC on purchases from unregistered suppliers, which makes voluntary registration commercially necessary in virtually every B2B business model.
What GST returns does an Indian startup need to file monthly?
Most registered Indian startups must file two monthly GST returns: GSTR-1 (outward supplies, declaring all invoices issued to GST-registered customers, due by the 11th) and GSTR-3B (summary return with net tax payment, due by the 20th). Additionally, GSTR-9 (annual return) is due by December 31st of the following financial year. Startups above ₹5Cr turnover must also file GSTR-9C (certified reconciliation statement).
What is TDS and which startup payments require TDS deduction?
TDS (Tax Deducted at Source) requires companies to deduct tax at source on certain payments and deposit it with the government. For Indian startups, the most common TDS obligations are: contractor payments above ₹30,000 (Section 194C — 1–2%), professional fees above ₹30,000 (Section 194J — 10%), rent above ₹2.4L/year (Section 194I — 10%), and salary payments (Section 192 — at applicable slab rates). TDS deposits are due by the 7th of the following month.
What ROC filings does a private limited startup need to make annually?
Every private limited company must file: AOC-4 (annual accounts) by November 29th, MGT-7 or MGT-7A (annual return) by November 28th, and DIR-3 KYC for every director by September 30th. Missing these deadlines attracts penalties of ₹100/day per filing. Startups that have raised funding should confirm whether their paid-up capital or turnover thresholds trigger additional requirements (statutory audit, Company Secretary appointment).
What is GST input tax credit and how does a startup claim it correctly?
Input tax credit (ITC) is the GST paid on purchases that a registered startup can offset against GST collected on sales. To claim ITC correctly: the vendor must have filed their GSTR-1 (the purchase must appear in the startup’s GSTR-2B); ITC must not be claimed on blocked categories (cars, club memberships, personal expenses); and GSTR-2B must be reconciled against the purchase ledger monthly. Komplai Managed performs this reconciliation as a standard month-end step, ensuring full ITC capture without over-claiming.
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